Data science through natural language with ChatGPT's Code Interpreter.

Large language models (LLMs) have emerged as a powerful tool for biomedical researchers, demonstrating remarkable capabilities in understanding and generating human-like text. ChatGPT with its Code Interpreter functionality, an LLM connected with the ability to write and execute code, streamlines data analysis workflows by enabling natural language interactions. Using materials from a previously published tutorial, similar analyses can be performed through conversational interactions with the chatbot, covering data loading and exploration, model development and comparison, permutation feature importance, partial dependence plots, and additional analyses and recommendations. The findings highlight the significant potential of LLMs in assisting researchers with data analysis tasks, allowing them to focus on higher-level aspects of their work. However, there are limitations and potential concerns associated with the use of LLMs, such as the importance of critical thinking, privacy, security, and equitable access to these tools. As LLMs continue to improve and integrate with available tools, data science may experience a transformation similar to the shift from manual to automatic transmission in driving. The advancements in LLMs call for considering the future directions of data science and its education, ensuring that the benefits of these powerful tools are utilized with proper human supervision and responsibility.

Trajectories of craving in the course of pharmacotherapy trials for methamphetamine use disorder.

AIMS: The aim of this study was to measure trajectories of craving for methamphetamine during the course of pharmacotherapy trials for methamphetamine use disorder. DESIGN, SETTING AND PARTICIPANTS: Craving trajectories were identified using Group-Based Trajectory Modeling. The association of craving trajectories with drug use trajectories was examined using a dual trajectory model. Association of craving trajectories with other health and social outcomes was also examined. The study used pooled data from five randomized controlled pharmacotherapy trials for methamphetamine use disorder. A total of 866 adults with methamphetamine use disorder participated in randomized controlled pharmacotherapy trials. MEASUREMENT: Craving was assessed weekly using the Brief Substance Craving Scale. Drug use was assessed using urine toxicology. Alcohol- and drug-related problems, as well as psychiatric, medical, legal, employment and relationship problems, were measured using the Addiction Severity Index. FINDINGS: A three-trajectory model with high, medium and low craving trajectories was selected as the most parsimonious model. Craving trajectories were associated with methamphetamine use trajectories in the course of trial; 88.4% of those in the high craving trajectory group had a consistently high frequency of methamphetamine use compared with 18.7% of those in the low craving group. High craving was also associated with less improvement in most other outcomes and higher rate of dropout from treatment. In turn, low craving was associated with a rapidly decreasing frequency of methamphetamine use, greater improvement in most other outcomes and a lower rate of dropout. Participants on modafinil daily and ondansetron 1 mg twice daily were less likely to be in the high craving group compared with those on placebo. CONCLUSIONS: Trajectories of methamphetamine craving in the course of clinical trials for methamphetamine use disorder appear to be both highly variable and strongly associated with greater frequency of drug use, other drug-related outcomes and dropout from trials. Two medications, modafinil daily and ondansetron at a dose of 1 mg two times daily, appear to be associated with greater reduction in craving in the course of treatment compared with placebo. A decrease in methamphetamine craving shows promise as an early indicator of recovery from methamphetamine use disorder.

Static and Dynamic Cross-Network Functional Connectivity Shows Elevated Entropy in Schizophrenia Patients.

Schizophrenia (SZ) patients exhibit abnormal static and dynamic functional connectivity across various brain domains. We present a novel approach based on static and dynamic inter-network connectivity entropy (ICE), which represents the entropy of a given network's connectivity to all the other brain networks. This novel approach enables the investigation of how connectivity strength is heterogeneously distributed across available targets in both SZ patients and healthy controls. We analyzed fMRI data from 151 schizophrenia patients and demographically matched 160 healthy controls. Our assessment encompassed both static and dynamic ICE, revealing significant differences in the heterogeneity of connectivity levels across available brain networks between SZ patients and healthy controls (HC). These networks are associated with subcortical (SC), auditory (AUD), sensorimotor (SM), visual (VIS), cognitive control (CC), default mode network (DMN) and cerebellar (CB) functional brain domains. Elevated ICE observed in individuals with SZ suggests that patients exhibit significantly higher randomness in the distribution of time-varying connectivity strength across functional regions from each source network, compared to healthy control group. C-means fuzzy clustering analysis of functional ICE correlation matrices revealed that SZ patients exhibit significantly higher occupancy weights in clusters with weak, low-scale functional entropy correlation, while the control group shows greater occupancy weights in clusters with strong, large-scale functional entropy correlation. k-means clustering analysis on time-indexed ICE vectors revealed that cluster with highest ICE have higher occupancy rates in SZ patients whereas clusters characterized by lowest ICE have larger occupancy rates for control group. Furthermore, our dynamic ICE approach revealed that it appears healthy for a brain to primarily circulate through complex, less structured connectivity patterns, with occasional transitions into more focused patterns. However, individuals with SZ seem to struggle with transiently attaining these more focused and structured connectivity patterns. Proposed ICE measure presents a novel framework for gaining deeper insights into understanding mechanisms of healthy and disease brain states and a substantial step forward in the developing advanced methods of diagnostics of mental health conditions.

Assessing the reactions of tourist markets to reinstated travel restrictions in the destination during the post-COVID-19 phase.

This study, leveraging search engine data, investigates the dynamics of China's domestic tourism markets in response to the August 2022 epidemic outbreak in Xinjiang. It focuses on understanding the reaction mechanisms of tourist-origin markets during destination crises in the post-pandemic phase. Notably, the research identifies a continuous rise in the potential tourism demand from tourist origin cities, despite the challenges posed by the epidemic. Further analysis uncovers a regional disparity in the growth of tourism demand, primarily influenced by the economic stratification of origin markets. Additionally, the study examines key tourism attractions such as Duku Road, highlighting its resilient competitive system, which consists of distinctive tourism experiences, economically robust tourist origins, diverse tourist markets, and spatial pattern stability driven by economic factors in source cities, illustrating an adaptive response to external challenges such as crises. The findings provide new insights into the dynamics of tourism demand, offering a foundation for developing strategies to bolster destination resilience and competitiveness in times of health crises.

Transcriptomics : Approaches to Quantifying Gene Expression and Their Application to Studying the Human Brain.

To date, the field of transcriptomics has been characterized by rapid methods development and technological advancement, with new technologies continuously rendering older ones obsolete.This chapter traces the evolution of approaches to quantifying gene expression and provides an overall view of the current state of the field of transcriptomics, its applications to the study of the human brain, and its place in the broader emerging multiomics landscape.

[Microbial metaproteomics--From sample processing to data acquisition and analysis].

Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.

[Research progress of deep learning applications in mass spectrometry imaging data analysis].

Mass spectrometry imaging (MSI) is a promising method for characterizing the spatial distribution of compounds. Given the diversified development of acquisition methods and continuous improvements in the sensitivity of this technology, both the total amount of generated data and complexity of analysis have exponentially increased, rendering increasing challenges of data postprocessing, such as large amounts of noise, background signal interferences, as well as image registration deviations caused by sample position changes and scan deviations, and etc. Deep learning (DL) is a powerful tool widely used in data analysis and image reconstruction. This tool enables the automatic feature extraction of data by building and training a neural network model, and achieves comprehensive and in-depth analysis of target data through transfer learning, which has great potential for MSI data analysis. This paper reviews the current research status, application progress and challenges of DL in MSI data analysis, focusing on four core stages: data preprocessing, image reconstruction, cluster analysis, and multimodal fusion. The application of a combination of DL and mass spectrometry imaging in the study of tumor diagnosis and subtype classification is also illustrated. This review also discusses trends of development in the future, aiming to promote a better combination of artificial intelligence and mass spectrometry technology.

Functional data geometric morphometrics with machine learning for craniodental shape classification in shrews.

This work proposes a functional data analysis approach for morphometrics in classifying three shrew species (S. murinus, C. monticola, and C. malayana) from Peninsular Malaysia. Functional data geometric morphometrics (FDGM) for 2D landmark data is introduced and its performance is compared with classical geometric morphometrics (GM). The FDGM approach converts 2D landmark data into continuous curves, which are then represented as linear combinations of basis functions. The landmark data was obtained from 89 crania of shrew specimens based on three craniodental views (dorsal, jaw, and lateral). Principal component analysis and linear discriminant analysis were applied to both GM and FDGM methods to classify the three shrew species. This study also compared four machine learning approaches (naïve Bayes, support vector machine, random forest, and generalised linear model) using predicted PC scores obtained from both methods (a combination of all three craniodental views and individual views). The analyses favoured FDGM and the dorsal view was the best view for distinguishing the three species.

Development and qualification of 3 L scale-down model for large scale vaccine process on vero cell culture using microcarriers.

Scale-down models (SDM) are pivotal tools for process understanding and improvement to accelerate the development of vaccines from laboratory research to global commercialization. In this study, a 3 L SDM representing a 50 L scale Vero cell culture process of a live-attenuated virus vaccine using microcarriers was developed and qualified based on the constant impeller power per volume principle. Both multivariate data analysis (MVDA) and the traditional univariate data analysis showed comparable and equivalent cell growth, metabolic activity, and product quality results across scales. Computational fluid dynamics simulation further confirmed similar hydrodynamic stress between the two scales.

Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be , has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.

Bayesian modeling of spatial ordinal data from health surveys.

Health surveys allow exploring health indicators that are of great value from a public health point of view and that cannot normally be studied from regular health registries. These indicators are usually coded as ordinal variables and may depend on covariates associated with individuals. In this article, we propose a Bayesian individual-level model for small-area estimation of survey-based health indicators. A categorical likelihood is used at the first level of the model hierarchy to describe the ordinal data, and spatial dependence among small areas is taken into account by using a conditional autoregressive distribution. Post-stratification of the results of the proposed individual-level model allows extrapolating the results to any administrative areal division, even for small areas. We apply this methodology to describe the geographical distribution of a self-perceived health indicator from the Health Survey of the Region of Valencia (Spain) for the year 2016.

The Impact of Sparse Datasets When Harmonizing Data from Studies with Different Measures of the Same Construct.

Prevention science has increasingly turned to integrative data analysis (IDA) to combine individual participant-level data from multiple studies of the same topic, allowing us to evaluate overall effect size, test and model heterogeneity, and examine mediation. Studies included in IDA often use different measures for the same construct, leading to sparse datasets. We introduce a graph theory method for summarizing patterns of sparseness and use simulations to explore the impact of different patterns on measurement bias within three different measurement models: a single common factor, a hierarchical model, and a bifactor model. We simulated 1000 datasets with varying levels of sparseness and used Bayesian methods to estimate model parameters and evaluate bias. Results clarified that bias due to sparseness will depend on the strength of the general factor, the measurement model employed, and the level of indirect linkage among measures. We provide an example using a synthesis dataset that combined data on youth depression from 4146 youth who participated in 16 randomized field trials of prevention programs. Given that different synthesis datasets will embody different patterns of sparseness, we conclude by recommending that investigators use simulation methods to explore the potential for bias given the sparseness patterns they encounter.

A robust CETSA data analysis automation workflow for routine screening.

The Cellular Thermal Shift Assay (CETSA) enables the study of protein-ligand interactions in a cellular context. It provides valuable information on the binding affinity and specificity of both small and large molecule ligands in a relevant physiological context, hence forming a unique tool in drug discovery. Though high-throughput lab protocols exist for scaling up CETSA, subsequent data analysis and quality control remain laborious and limit experimental throughput. Here, we introduce a scalable and robust data analysis workflow which allows integration of CETSA into routine high throughput screening (HT-CETSA). This new workflow automates data analysis and incorporates quality control (QC), including outlier detection, sample and plate QC, and result triage. We describe the workflow and show its robustness against typical experimental artifacts, show scaling effects, and discuss the impact of data analysis automation by eliminating manual data processing steps.

The impact of national savings on economic development: a focused study on the ten poorest countries in Sub-Saharan Africa.

The purpose of this study is to examine the impact of national savings on economic development, as measured by the Human Development Index (HDI), Inequality-adjusted HDI (iHDI), and Multidimensional Poverty Index (MPI), in ten of the poorest countries in Sub-Saharan Africa. The study employs a sequential Generalized Method of Moments (GMM) analysis to address potential endogeneity issues and account for the dynamic nature of the relationships, covering the period from 2009 to 2019. The findings reveal a complex relationship between national savings and the selected development indicators. While national savings exhibit positive impacts on HDI and iHDI, the results are not consistently statistically significant across all the sequential models. However, the analysis suggests that national savings have a positive influence on reducing multidimensional poverty, as measured by MPI, particularly when effectively channeled into productive investments. The study also highlights the significant positive impact of government expenditure and foreign direct investment (FDI) on human development, underscoring the importance of strategic public investments and foreign capital. The results suggest that while national savings are crucial, their effective utilization is essential for enhancing human development indices. Strategic investments in public goods and foreign capital are also important. The mixed effects of inflation and official development assistance (ODA) emphasize the need for stable economic policies and effective utilization of foreign aid. The modest positive impact of institutional quality suggests that improvements in governance and institutional frameworks can contribute to human development. The findings underscore the need for policies promoting financial inclusion, efficient public expenditure, foreign direct investment, and stable macroeconomic conditions to leverage national savings for economic development. The study's findings provide valuable insights for policymakers in Sub-Saharan Africa, highlighting the need for comprehensive strategies that leverage national savings, public expenditure, and foreign investment to drive sustainable economic development and poverty reduction.

Exploring Relations Between Unique Patient Characteristics and Virtual Reality Immersion Level on Anxiety and Pain in Patients Undergoing Venipuncture: Secondary Analysis of a Randomized Control Trial.

BACKGROUND: Virtual reality (VR) is a well-researched digital intervention that has been used for managing acute pain and anxiety in pediatric patients undergoing various medical procedures. This study focuses on investigating the role of unique patient characteristics and VR immersion level on the effectiveness of VR for managing pediatric pain and anxiety during venipuncture. OBJECTIVE: The purpose of this study is to determine how specific patient characteristics and level of immersion during a VR intervention impact anxiety and pain levels for pediatric patients undergoing venipuncture procedures. METHODS: This study is a secondary data analysis of 2 combined, previously published randomized control trials on 252 pediatric patients aged 10-21 years observed at Children's Hospital Los Angeles from April 12, 2017, to July 24, 2019. One randomized clinical trial was conducted in 3 clinical environments examining peripheral intravenous catheter placement (radiology and an infusion center) and blood draw (phlebotomy). Conditional process analysis was used to conduct moderation and mediation analyses to assess the impact of immersion level during the VR intervention. RESULTS: Significant moderation was found between the level of immersion and anxiety sensitivity when predicting postprocedural anxiety (P=.01). Patients exhibiting the highest anxiety sensitivity within the standard of care yielded a 1.9 (95% CI 0.9-2.8; P<.001)-point elevation in postprocedural anxiety relative to individuals with high immersion levels. No other significant factors were found to mediate or moderate the effect of immersion on either postprocedural anxiety or pain. CONCLUSIONS: VR is most effective for patients with higher anxiety sensitivity who report feeling highly immersed. Age, location of the procedure, and gender of the patient were not found to significantly impact VR's success in managing levels of postprocedural pain or anxiety, suggesting that immersive VR may be a beneficial intervention for a broad pediatric population. TRIAL REGISTRATION: ClinicalTrials.gov NCT04268901; https://clinicaltrials.gov/study/NCT04268901.

Using Conditional Entropy Networks of Ordinal Measures to Examine Changes in Self-Worth Among Adolescent Students in High School.

We implement an analytic approach for ordinal measures and we use it to investigate the structure and the changes over time of self-worth in a sample of adolescents students in high school. We represent the variations in self-worth and its various sub-domains using entropy-based measures that capture the observed uncertainty. We then study the evolution of the entropy across four time points throughout a semester of high school. Our analytic approach yields information about the configuration of the various dimensions of the self together with time-related changes and associations among these dimensions. We represent the results using a network that depicts self-worth changes over time. This approach also identifies groups of adolescent students who show different patterns of associations, thus emphasizing the need to consider heterogeneity in the data.

Artificial intelligence for automatic detection and segmentation of nasal polyposis: a pilot study.

PURPOSE: Accurate diagnosis and quantification of polyps and symptoms are pivotal for planning the therapeutic strategy of Chronic rhinosinusitis with nasal polyposis (CRSwNP). This pilot study aimed to develop an artificial intelligence (AI)-based image analysis system capable of segmenting nasal polyps from nasal endoscopy videos. METHODS: Recorded nasal videoendoscopies from 52 patients diagnosed with CRSwNP between 2019 and 2022 were retrospectively analyzed. Images extracted were manually segmented on the web application Roboflow. A dataset of 342 images was generated and divided into training (80%), validation (10%), and testing (10%) sets. The Ultralytics YOLOv8.0.28 model was employed for automated segmentation. RESULTS: The YOLOv8s-seg model consisted of 195 layers and required 42.4 GFLOPs for operation. When tested against the validation set, the algorithm achieved a precision of 0.91, recall of 0.839, and mean average precision at 50% IoU (mAP50) of 0.949. For the segmentation task, similar metrics were observed, including a mAP ranging from 0.675 to 0.679 for IoUs between 50% and 95%. CONCLUSIONS: The study shows that a carefully trained AI algorithm can effectively identify and delineate nasal polyps in patients with CRSwNP. Despite certain limitations like the focus on CRSwNP-specific samples, the algorithm presents a promising complementary tool to existing diagnostic methods.

Spectroscopic Benchmarks by Machine Learning as Discriminant Analysis for Unconventional Italian Pictorialism Photography.

Up to the 1930s, the Italian pictorialism movement dominated photography, and many handcrafted procedures started appearing. Each operator had his own working method and his own secrets to create special effects that moved away from the standard processes. Here, a methodology that combines X-ray fluorescence and infrared analysis spectroscopy with unsupervised learning techniques was developed on an unconventional Italian photographic print collection (the Piero Vanni Collection, 1889-1939) to unveil the artistic technique by the extraction of spectroscopic benchmarks. The methodology allowed the distinction of hidden elements, such as iodine and manganese in silver halide printing, or highlighted slight differences in the same printing technique and unveiled the stylistic practice. Spectroscopic benchmarks were extracted to identify the elemental and molecular fingerprint layers, as the oil-based prints were obscured by the proteinaceous binder. It was identified that the pigments used were silicates or iron oxide introduced into the solution or that they retraced the practice of reusing materials to produce completely different printing techniques. In general, four main groups were extracted, in this way recreating the 'artistic palette' of the unconventional photography of the artist. The four groups were the following: (1) Cr, Fe, K, potassium dichromate, and gum arabic bands characterized the dichromate salts; (2) Ag, Ba, Sr, Mn, Fe, S, Ba, gelatin, and albumen characterized the silver halide emulsions on the baryta layer; (3) the carbon prints were benchmarked by K, Cr, dichromate salts, and pigmented gelatin; and (4) the heterogeneous class of bromoil prints was characterized by Ba, Fe, Cr, Ca, K, Ag, Si, dichromate salts, and iron-based pigments. Some exceptions were found, such as the baryta layer being divided into gum bichromate groups or the use of albumen in silver particles suspended in gelatin, to underline the unconventional photography at the end of the 10th century.

Gradient synchronization for multivariate functional data, with application to brain connectivity.

Quantifying the association between components of multivariate random curves is of general interest and is a ubiquitous and basic problem that can be addressed with functional data analysis. An important application is the problem of assessing functional connectivity based on functional magnetic resonance imaging (fMRI), where one aims to determine the similarity of fMRI time courses that are recorded on anatomically separated brain regions. In the functional brain connectivity literature, the static temporal Pearson correlation has been the prevailing measure for functional connectivity. However, recent research has revealed temporally changing patterns of functional connectivity, leading to the study of dynamic functional connectivity. This motivates new similarity measures for pairs of random curves that reflect the dynamic features of functional similarity. Specifically, we introduce gradient synchronization measures in a general setting. These similarity measures are based on the concordance and discordance of the gradients between paired smooth random functions. Asymptotic normality of the proposed estimates is obtained under regularity conditions. We illustrate the proposed synchronization measures via simulations and an application to resting-state fMRI signals from the Alzheimer's Disease Neuroimaging Initiative and they are found to improve discrimination between subjects with different disease status.

Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol.

Chromatin immunoprecipitation (ChIP) is an invaluable method to characterize interactions between proteins and genomic DNA, such as the genomic localization of transcription factors and post-translational modification of histones. DNA and proteins are reversibly and covalently crosslinked using formaldehyde. Then the cells are lysed to release the chromatin. The chromatin is fragmented into smaller sizes either by micrococcal nuclease (MN) or sonication and then purified from other cellular components. The protein-DNA complexes are enriched by immunoprecipitation (IP) with antibodies that target the epitope of interest. The DNA is released from the proteins by heat and protease treatment, followed by degradation of contaminating RNAs with RNase. The resulting DNA is analyzed using various methods, including polymerase chain reaction (PCR), quantitative PCR (qPCR), or sequencing. This protocol outlines each of these steps for both yeast and human cells. This chapter includes a contextual discussion of the combination of ChIP with DNA analysis methods such as ChIP-on-Chip, ChIP-qPCR, and ChIP-Seq, recent updates on ChIP-Seq data analysis pipelines, complementary methods for identification of binding sites of DNA binding proteins, and additional protocol information about ChIP-qPCR and ChIP-Seq.